From baa2845d2818066bcbd8b91e6ce77d71e36ecf45 Mon Sep 17 00:00:00 2001
From: Lucpen <lucia.pena.perez@scilifelab.se>
Date: Thu, 25 Aug 2022 12:06:02 +0200
Subject: [PATCH] Included args option in picard AddOrReplaceReadGroups (#1973)

feat included args option in picard addorreplacereadgroups
---
 modules/picard/addorreplacereadgroups/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf
index 8e9bda07..116aa4fa 100644
--- a/modules/picard/addorreplacereadgroups/main.nf
+++ b/modules/picard/addorreplacereadgroups/main.nf
@@ -34,8 +34,9 @@ process PICARD_ADDORREPLACEREADGROUPS {
     }
     """
     picard \\
-        AddOrReplaceReadGroups \\
         -Xmx${avail_mem}g \\
+        AddOrReplaceReadGroups \\
+        $args \\
         --INPUT ${bam} \\
         --OUTPUT ${prefix}.bam \\
         --RGID ${ID} \\